Bioconductor Forum

Dear dr. Stark and community, I'm using Diffbind to obtain differential expression values for a series of interesting regions and I have some questions.I run...Dear dr. Stark and community, I'm using Diffbind to obtain differential expression values for a series of interesting regions and I have some questions.I run the

diffbind normalization

updated 10.6 years ago • eva.pinatel

K27ac, and K4me1. We carried out peak calling using SEACR and then differential peak calling using Diffbind. Now, we want to go back to the raw peak data and just plot the normalized peak data. Can i use the dba.normalize function...to ChipSeeker so I can plot it. I don't know if this is a naive question because I went through the diffbind tutorial and couldn't find anything specific to normalizi…

Normalization Peakdata DiffBind Cut&Tag

updated 3.3 years ago • bhandary.8590

Hi,  I am having some trouble with the dba.count function in Diffbind dba.count function. See below:  <pre> DBA.count = dba.count(DBA, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot

diffbind

updated 7.2 years ago • loretta

<div class="preformatted"> Hello I am using DiffBind to identify consensus binding sites for multiple transcription factors that have biological replicates. In addition...div class="preformatted"> Hello I am using DiffBind to identify consensus binding sites for multiple transcription factors that have biological replicates. In

DiffBind DiffBind

updated 12.2 years ago • Guest User

with the Encode ATACseq pipeline. I now want to call differentially opened chromatin regions with DiffBind, but it gives me an error when I want to normalize. Also when I run dba.analyze, it gives me the same error. I don't understand...what I am doing wrong? I appreciate any input! best, Ben ```r library(DiffBind) dir <- "/staging/leuven/stg_00072/Ben/ATACseq" setwd(dir) ## read in …

DiffBind

updated 4.7 years ago • ben.vanderveer

Hey, I saved a first chipQC object using consensus=TRUE,bCounts=TRUE,summits=250 options. Then I reused it latter inside DiffBind. __First I was wondering if it uses score or count to make heatmap ? Documentation it misleading, it is said it uses scores...chipQC object using consensus=TRUE,bCounts=TRUE,summits=250 options. Then I reused it latter inside DiffBind. __First I was wondering if i…

diffbind

updated 8.4 years ago • ZheFrench

Hi folks, I am having a trouble with dba.count function in diffbind. It fails with warnings but without any specific information. Please see below: > obj <- dba(sampleSheet='analysis...nbsp;methods   \[9\] base      other attached packages:  \[1\] DiffBind\_2.4.8             S…

DiffBind dba.count Chip-Seq Differential analysis

updated 4.8 years ago • urjaswita

in diffbind when perform this: tamoxifen <- dba.contrast(tamoxifen,+ reorderMeta=list(Condition="Responsive")) then at the results

BASiCS

updated 15 months ago • Jeffcgen2000

that we can use for the analysis of differential binding ? (I do not have access to the packages DiffBind or derfinder) ; much thanks, Bogdan

DESeq2 edgeR bigwig limma

updated 3.3 years ago • Bogdan

I am trying out different DiffBind normalization methods for my ATAC-seq dataset in order to select the most suitable one. However, it looks like no...I am trying out different DiffBind normalization methods for my ATAC-seq dataset in order to select the most suitable one. However, it looks like no matter

ATACSeq Normalization DiffBind

updated 3.8 years ago • bers.anthrope

Hi, I am using dba.plotvenn to plot overlapped binding sites between three groups. I have created a three-way Venn diagram, but I do not like how it looks. As the picture shows, numbers "16782" and "5632" are not where they are supposed to be. Also, group #2 is on the line, which needs to be shifted to the right a bit. I am looking everywhere, but the answer is nowhere. Please help …

diffbind plot venn diagram

updated 5.3 years ago • jiekwo1

Hi! I am trying to run Diffbind with DESeq2 on my Cut&Run dataset. I have tried multiple normalization methods in dba.count() and dba.normalize

DiffBind volcanoplot Normalization Cut&Run

updated 23 months ago • be308df4

I would like to compare two conditions with each two ChIP-seq (H3K27me3) samples. I searched for tools for differential binding and found that many including diffbind and csaw compares two conditions with read counts from pull down library only, not using input/control library/read...seq (H3K27me3) samples. I searched for tools for differential binding and found that many including diffbind and c…

diffbind csaw

updated 7.6 years ago • bioinfo

Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I  import the bed file data into a DiffBind DBA object using the command > dbaObj <-  dba(sampleSheet = "samples.csv") The problem is that the chromosome names...chr11, chr12, chr13, chr13\_random, chr14…

DiffBind ChIP-Seq

updated 11.2 years ago • Georg Otto

function, and subsequently dba.analyze(). I basically followed the steps on page 45 of the Diffbind documentation. https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf However...or scripts of runnning successful offset and loess normalization? Thank you! ```r library(DiffBind) library(edgeR) library(tidyverse) library(dplyr) samples <…

DiffBind Normalization

updated 21 months ago • Henry

Hello! I am currently using DiffBind 3.6.1 and encountering the following error when attempting to analyze my data: ```r > dba <- dba.contrast(dba, design

DiffBind

updated 3.6 years ago • millerh1

Hello there, I am just started playing with ChIPQC and DiffBind but I am failing miserably at just loading the sample data.  I have downloaded the DiffBind Package data from...your website (https://www.dropbox.com/s/gfc49wul2bv5nz6/DiffBind\_vignette\_data.tar.gz) My script looks like: <pre> # load libraries library(ChIPQC) library(DiffBind) # read in files

ChipQC diffbind

updated 7.4 years ago • avp25

files i.e `125`. P.S: from github the error stems from this section : https://github.com/aeron15/DiffBind/blob/master/R/counts.R#L579 but I'm not familiar with what those lines mean. R version 4.1.0 (2021-05-18) Platform: x86_64

DiffBind

updated 4.6 years ago • Alexandre

compare them to identify enriched regions. In the case, can I use default DESeq2 pipeline similar as DiffBind ? Or Do I need to use one-sided test for enriched regions ? As I understand, if I want to check both enriched or depleted

deseq2 diffbind

updated 5.8 years ago • bioinfo

Hello, I've been using DiffBind for my analyses and it's working great, apart from a specific problem I encountered with the output: Sometimes it...Hello, I've been using DiffBind for my analyses and it's working great, apart from a specific problem I encountered with the output: Sometimes it will

DiffBind

updated 4.0 years ago • mhw46

<div class="preformatted">Hi Alejandra- First, can you check the versions you are using by sending the output of sessionInfo()? The color bars were added to DiffBind at some point and are not present in all versions. You need version 1.4.0 or later, which corresponds to Bioconductor 2.11 (R 2.15). Next, check the help page for dba.plotHeatmap: > ?dba.plotHeatmap All of the heatma…

Category DiffBind Category DiffBind

updated 12.7 years ago • Rory Stark

Dear Rory Stark, Thanks for DiffBind package for analyzing ChIP-seq dataset that has multiple replicates. I encountered two issues when trying to add

diffbind

updated 7.2 years ago • yuhongning2013

Hi I had a question about the following example in the diffbind tutorial: # Plot effect of a range of filter values and then apply filter data(tamoxifen_counts) rate.max <- dba.count

diffbind

updated 6.3 years ago • rbronste

Conc**(which is showed in final dba.report) and **score**. Let's make a example ``` library(DiffBind) library(BiocParallel) library(dplyr) tamoxifen <- dba(sampleSheet="tamoxifen.csv") tamoxifen <- dba.count(tamoxifen

DiffBind

updated 5.0 years ago • shangguandong1996

Hi, I'm trying to run DiffBind `3.4.11` on R `4.1.2` on some bed files created using bedtools merge, so they look like: ```r 1 1875658 1934008 EdU_HU_HME1_sgMSL1_R1_peak_54

DiffBind

updated 3.2 years ago • Pablo

Hi there, Thank you for developing DiffBind package! I am running through the vignette. It is really helpful. I see the codes using `dbs.all` in Section 7.5. But I...Hi there, Thank you for developing DiffBind package! I am running through the vignette. It is really helpful. I see the codes using `dbs.all` in Section 7.5. But I do

DiffBind

updated 4.0 years ago • Mark

Enter the body of text here Code should be placed in three backticks as shown below ```r # include your problematic code here with any corresponding output # please also include the results of running the following in an R session sessionInfo( ) cell <- dba(sampleSheet = "/home/cytolab/extdata/cell lines data.csv") 1 cal27 ko1 H3K36me2 Treated full media 1 bed Error in if (file.info(pe…

DiffBind chipseq

updated 2.5 years ago • ANAMIKA

I have a very simple question: how can I check my version of an installed package - in this case DiffBind? I know a simple `-v` in Unix achieves this, but I can't seem to figure it out in R. Part of the reason I need to know is because

DiffBind

updated 5.0 years ago • bertb

Hi All, I have Chip-Seq data for histone marks (H3K27me3, H3K27ac, H3K4me1 and H3K4me3) for 2 different cancer subtypes which differ in their aggressiveness. I am interested to see if there is any association between the tumor aggressiveness and H3K27me3 loss. I have used Diffbind to call differential binding sites between different subtypes for each antibody. I read it somewhere that the H3K…

Chip Seq Histone H3K27me3 macs diffbind

updated 6.4 years ago • researcher

Hello Everyone,   Let me start by saying I've read all posts that are similar to my question and the insights are tremendous! However, as I've been doing bioinformatics for a little over a year now, I'm still a newbie in all possible respects, and I just want a clarification.   So here's the gist. I have replicates of three conditions (each with its own Input). What I first …

deseq2 diffbind csaw greylistchip chipseq

updated 7.1 years ago • Yonatan Amzaleg

sequence coverage difference between replicates and among samples? I am using DESeq2 and edgeR in DiffBind to compare ATAC-seq samples with different sequencing coverage among samples, from 77 to 25 million reads, and up

DESeq2 edgeR DiffBind

updated 3.2 years ago • cesar.arenasmena

Hello All, I have 300 chIP peaksets. I am trying to count and analyze them using DiffBind. However when I am running the code, I get the following error. Will appreciate any suggestion to fix it. Many thanks

DiffBind chip-seq differentially-binding-site

updated 5.3 years ago • Mar Mar

dds)) > 10, ]</pre> I obtain the count matrices from ChIP-seq and ATAC-seq experiments through DiffBind and then use DESeq2 for the differential binding analysis. I guess its a bit of an arbitrary cutoff, but wondering

deseq2 atac-seq chipseq differential binding analysis

updated 8.1 years ago • rbronste

div class="preformatted">Hi I have been trying to use DiffBind to analyze our Chip-seq data and have been running into some errors repeatedly. I first created a samplesheet.csv...each and the peaks were called using MACS v2. The peak caller generated .bed files which was used in DiffBind. I defined the working directory in R first. I then read the sample sheet in : > H3K4.B73=dba(s…

DiffBind DiffBind

updated 12.4 years ago • Anitha Sundararajan

please help me, I will be very grateful.  I am trying to do the dba.count command out of the DiffBind package in R. Creating the dba object works fine for me, but when I wanted to do the counting, this error occurs: > counts.runx1...nbsp;   datasets  methods   base      other attached packages: \[1\] DiffBind\_1.8.5 &…

R diffbind

updated 8.8 years ago • jorrenkuster

Hello, I am running DiffBind analysis on a ChIP-Seq dataset, comparing Control versus Treatment and using Factor(Donor IDs) as a blocking factor...of estimateDispersionsFit within the DESeq2 model. How do I implement this change through DiffBind? *** ####My code: dat.bind <- dba.contrast(dat.bind, group1=dat.bind$masks$cond1, group2=dat.bind$masks$cond0, name1=cond1...…

diffbind

updated 7.0 years ago • avantika6194

I am attempting to perform differential peak analysis from ATAC-seq data using DiffBind package and am running into problems with the dba.count function. I have 2 conditions (rapid vs slow) with 3 samples

DiffBind

updated 6.4 years ago • chadnewton

analyzing large data set and to speed up things I am going to use cluster.  I am working with DiffBind packadge and I will create a single GRanges object that will be used for dba.counts function to create few smaller

Diffbind

updated 7.7 years ago • Lauma R

the same problem?</span>     <span style="line-height:1.6">I have </span> DiffBind\_1.10.2 version and R version 3.1.0   <span style="line-height:1.6">Thanks in advance. </span>   <span style

DiffBind diffbind

updated 11.2 years ago • sergio.espeso-gil

Hi Rory,     I am trying diffBind on my ATAC-seq data. And I have difficulties on using db.count() function. I got error message as below. Error in pv.counts

edger

updated 10.8 years ago • yijing.su

Hello, I have a question about figure 13 in the Diffbind manual.  according to this part (page4, > tamoxifen <- dba(sampleSheet="tamoxifen.csv") :  3 MCF71 MCF7...Hello, I have a question about figure 13 in the Diffbind manual.  according to this part (page4, > tamoxifen <- dba(sampleSheet="tamoxifen.csv") :  3 …

diffbind

updated 8.6 years ago • mforoo1

with 12 bed files, i get this from str(dba): ```$ totalMerged: int 42967 $ called : num [1:42967, 1:12] 0 1 1 1 0 0 1 1 1 1 ... $ merged : num [1:42967, 1:3] 1 1 1 1 1 1 1 1 1 1 ... ``` with 11 bed files, i get this from str(dba): ```$ totalMerged: int 42967 $ called : num [1:3477, 1:11] 0 0 0 0 0 0 0 0 0 0 ... $ merged : num [1:42967, 1:3] 1 1 1 1 1 1 1 1 1 1 ... ``` wha…

diffbind dba

updated 3.5 years ago • Nicole

I have 10 "summit" bed files from macs2 peak-calling, with 5 factors with 2 replicates each. I added them all one-by-one to a dba object "dbObj" that looks like this: 10 Samples, 3202 sites in matrix (234027 total): ID Factor Replicate Caller Intervals 1 CTR-1 ctr 1 bed 29940 2 CTR-2 ctr 2…

diffbind chipseq

updated 5.9 years ago • hkitano

Trying to set up a contrast based on some masks and having some problems. The __dba.count__ looks as follows: 12 Samples, 1054182 sites in matrix (2657422 total): ID Tissue Factor Condition Treatment Replicate Caller Intervals

1  MBV1  BN1     DR      MALE   VEHICLE         1 narrow    500000

2  MBV2  BN1     DR      MALE   VEHICLE         2 narrow    281265

3…

diffbind chipseq

updated 8.4 years ago • rbronste

When you retrieve the differentially bound sites with `` dba.report() ``, there is a "Conc" column that shows the mean read concentration over all the samples (log2 normalized ChIP read counts with control read counts subtracted). Is there a way to calculate those numbers for arbitrary regions (not just differentially bound)?

diffbind chipseq

updated 10.6 years ago • igor

Trying to generate replicate masks for the dba.count function from a .csv where I list 3 replicates under DBA\_CONDITION. Want to do dba.counts with minMembers = 3 to include only those that are in all 3 of each replicate group for the binding matrix. Any clues on how to do this? Thanks.

diffbind chipseq

updated 8.4 years ago • rbronste

Hi ! Hi I want to draw a venn diagram of the peaks shared across four Tissues in my data set, but I'm not able to correctly select the set of peaks or create a contrast that achieves this. The idea is to get four way vennDiagram with the four Tissues. I have tried different things > Example.data <- dba(sampleSheet=Example.table, minOverlap=1) > Example.data.counts <- dba.count…

diffbind chip-seq

updated 10.0 years ago • medinaale

Hi Rory, I had been previously, not marking duplicates or removing them in my ChIP-Seq datasets, and instead setting the dba.count bRemoveDuplicates to TRUE. Firstly, how adverse is this strategy when determining differential peaks? And secondly, how does setting bUseSummarizeOverlaps to TRUEcompare to bRemoveDuplicates? Thanks,

diffbind dba.count bRemoveDuplicates bUseSummarizeOverlaps

updated 6.9 years ago • loretta

Hi all, so I got the following from ATAC-seq samples > ATAC_seq_Goett_peaks 11 Samples, 47306 sites in matrix: ID Tissue Factor Replicate Caller Intervals FRiP 1 Cell1px8old epithelial Cell1 1 counts 47306 0.19 2 Cell1_3rd epithelial Cell1 2 counts 47306 0.18 3 Cell1px11new epithelial Cell1 …

diffbind plotVenn

updated 6.3 years ago • theodore.georgomanolis

I tried running the dba.count function and got the following error message? The bam files seem to be fine. ---

> chip_seq=chip_seq(tamoxifen,summit=250)

Error: Error processing one or more read files. Check warnings().

In addition: There were 28 warnings (use warnings() to see them)

> warnings()

Warning messages:

1: 

2: 

3: 

4: 

5: 

6: 

7: 

8…

diffbind

updated 7.8 years ago • hhhcce

Hi, I just wanted to get some clarification on MA plots and exactly what they represent. Including one I made of my diff peak data. I am wondering what the darker blue area is close to the origin as well as further down the log concentration and exactly what it represents in comparison with the lighter blue? Also maybe in this context what is the log concentration representing? Thanks for the cl…

diffbind ma plot

updated 8.9 years ago • rbronste

Hello, I am trying to calculate the FRiP score through `` dba.count() `` method as following, and I've been continuously getting this warning: > compareCount <- dba.count(compare, bParallel=FALSE) Sample: trimmed_DKO_R1.fastq.gz.sam.sort.clean.bam125 Sample: trimmed_DKO_R2.fastq.gz.sam.sort.clean.bam125 Sample: trimmed_HCT116_R1.fastq.gz.sam.sort.…

diffbind parallel

updated 8.0 years ago • ghosos

Hi, bam files for example execution are missing through installation. How can I find these test bams? Thanks, Kübra

diffbind reads bamfiles

updated 8.8 years ago • kbrnrc

div class="preformatted"> I have been trying to use DiffBind to analyze our Chip-seq data and have been running into some errors repeatedly. I first created a samplesheet.csv...each and the peaks were called using MACS v2. The peak caller generated .bed files which was used in DiffBind. I defined the working directory in R first. I then read the sample sheet in : > H3K4.B73=dba(sampleS…

DiffBind DiffBind

updated 12.4 years ago • Guest User

Hi all, I have a questions about bulk ATAc seq that could not find out myself and also on Biostar. I use Diffbind to get the table below (differential accessibility regions) and then use ChipPeakAnno to annotate the peaks in the...I have a questions about bulk ATAc seq that could not find out myself and also on Biostar. I use Diffbind to get the table below (differential accessibility regions) a…

ChIPpeakAnno DiffBind

updated 2.4 years ago • Chris

    Having trouble to get the ChIPQC to work properly. My ultimate goal is to have the html report generated using ChIPQCreport(). I read in the bam files through dba function in the DiffBind package. All went well and I was able to run all DiffBind functions. Using the same sample sheet and dba object does not work with ChIPQC.  I tried read in sample shee…

chipqc chipqcreport

updated 7.4 years ago • molly_the_minotaur

the problem, I have tried to use a csv table and also a single sample and even using dba object from DiffBind , but I have always this error message:   \[bam\_index\_load\] fail to load BAM index. Error: 16 errors; first error: &nbsp

ChIPQC

updated 11.0 years ago • sergio.espeso-gil

Hi, I have a error from dba.count DBdata <- dba.count(DBdata,summits = TRUE) Computing summits... Error in pv$called[, mask] : subscript out of bounds Can you let me know how to fix this? Thank you!

.

updated 4.3 years ago • Yoon Hee

Dear friends, While I was using the latest release (3.13), I have met a few problems which need your help. 1. I have repeated the whole process following the vignettes using the built in data sets, but my final results (I got 246 significantly differentially binding sites, see the attached file) are different from numbers (249) provided by the vignettes . 2. Those 246 sites w…

DiffBind

updated 4.6 years ago • skyyks123

Hello, am wondering if it is possible to call the function dba.contrast without the controls files (i do not have them). I have created a DBA odject as follow: mESC <- dba.peakset(NULL, bamReads = "/home/tandrean/Desktop/mESC/1.sorted.bam", bamControl = NULL, peaks="/home/tandrean/Desktop/mESC/1.test\_peaks…

Control Usage input files

updated 9.0 years ago • fusion.slope